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After you beat the Prototype, you will unlock a pair of bonus fields. In one of these, Robot Masters, including Robot Masters that are unfinished, will appear. This includes Mega Man 3's Robot Masters.

You must engage these Robots in combat, and when one steps up to fight you, hit them with a Copy Shot from a Copy Core Robot. In this way, you can earn their weapons and have them added to your arsenal.

Copy shot is your best friend in that case but Leveling up other robot masters at the same time can unlock more weapons for you easily if you have pretty low robot masters just have them join your best character in a battle and let them take some experience.